/EXTERNAL Roadmap/variants/K012807_1_lane_gembs
BACK
SAMPLE K012807_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1162517222 |
1008897353 |
86.79 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1162517222 |
100% |
1136825834 |
97.79 % |
25691388 |
2.21 % |
| |
|
|
|
|
|
|
| Passed |
1011144276 |
86.98 % |
1005394877 |
88.44 % |
5749399 |
0.57 % |
| Filtered |
151372946 |
13.02 % |
131430957 |
11.56 % |
19941989 |
1.97 % |
| |
|
|
|
|
|
|
| q20 |
100714997 |
66.53 % |
99273058 |
75.53 % |
1441939 |
7.23 % |
| q20,qd2 |
23065943 |
15.24 % |
5523851 |
4.20 % |
17542092 |
87.97 % |
| q20,mq40 |
16407076 |
10.84 % |
16269063 |
12.38 % |
138013 |
0.69 % |
| mq40 |
5847572 |
3.86 % |
5520573 |
4.20 % |
326999 |
1.64 % |
| q20,qd2,mq40 |
3302345 |
2.18 % |
3070053 |
2.34 % |
232292 |
1.16 % |
| qd2 |
1990950 |
1.32 % |
1739654 |
1.32 % |
251296 |
1.26 % |
| qd2,mq40 |
43163 |
0.03 % |
34705 |
0.03 % |
8458 |
0.04 % |
| qd2,fs60,mq40 |
413 |
0.00 % |
0 |
0.00 % |
413 |
0.00 % |
| fs60,mq40 |
200 |
0.00 % |
0 |
0.00 % |
200 |
0.00 % |
| qd2,fs60 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| q20,qd2,fs60,mq40 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| fs60 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
10843177 |
39.61 % |
| Transition |
G>A |
All |
1724756 |
6.30 % |
| Transition |
T>C |
All |
10155714 |
37.10 % |
| Transition |
C>T |
All |
1737341 |
6.35 % |
| Transversion |
A>C |
All |
244355 |
0.89 % |
| Transversion |
C>A |
All |
513387 |
1.88 % |
| Transversion |
T>G |
All |
254564 |
0.93 % |
| Transversion |
G>T |
All |
502655 |
1.84 % |
| Transversion |
A>T |
All |
452633 |
1.65 % |
| Transversion |
T>A |
All |
454737 |
1.66 % |
| Transversion |
C>G |
All |
249585 |
0.91 % |
| Transversion |
G>C |
All |
243382 |
0.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
936612 |
20.19 % |
| Transition |
G>A |
Passed |
699086 |
15.07 % |
| Transition |
T>C |
Passed |
893189 |
19.26 % |
| Transition |
C>T |
Passed |
703900 |
15.17 % |
| Transversion |
A>C |
Passed |
177303 |
3.82 % |
| Transversion |
C>A |
Passed |
183900 |
3.96 % |
| Transversion |
T>G |
Passed |
177866 |
3.83 % |
| Transversion |
G>T |
Passed |
184070 |
3.97 % |
| Transversion |
A>T |
Passed |
160697 |
3.46 % |
| Transversion |
T>A |
Passed |
160477 |
3.46 % |
| Transversion |
C>G |
Passed |
180456 |
3.89 % |
| Transversion |
G>C |
Passed |
181039 |
3.90 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
8.39 |
24460988 |
2915298 |
| Passed |
2.30 |
3232787 |
1405808 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |